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<body style="padding:20px;width:650px;font-family:Times">
<title>Sequence Result Table</title>
<h1>Sequence Result Table</h1>
Shows search results from "Filters" or "Show All". 
<h3>Add/remove columns</h3>
Change columns as follows: 
<ul>
<li>Select "Columns" link on the left panel. 
<li>Return to the desired table (selecting its tab on the left).
<li>Selecting "Refresh Columns" will redraw the table with the altered column selection.
</ul>
<h3>Sorting</h3>
Columns may be sorted ascending or descending. Click on the header once for descending,
then again for ascending; or, right-click for ascending. <b>Note</b>: The DE columns have 
negative and positive values, where negative means the first library has read count less
than the second. The sort on the DE column ignores the sign so the right click sorts all
DE to the top.
<h3>Column re-order</h3>
Columns may dragged to different positions, by clicking and dragging the headers.
<h3>Export</h3>
The table data can be exported to a file with 6 different options:
<ul>
<li><b>Table of columns:</b> tab-delimited copy of the table
<li><b>Sequences from table:</b> fasta file of all the sequences 
<li><b>Translated ORFs:</b> fasta file of coding sequences (i.e., ORFs) found in 
the sequences in the table (note, a sequence may not have an identifiable ORF)
<li><b>Read counts:</b> export counts in MeV format
<li><b>PCC of RPKM/log2(RPKM):</b> compute pairwise Pearson correlation (described below)
<li><b>GOs from table:</b> list GOs associated to sequences in the table (enter single level or range e.g. 2-5)
</ul>
<h3>Copy</h3>
Copies the table to the clipboard, which can then be pasted into a file.
<h3>Pearson correlations</h3>
A common way to cluster sequences for e.g. network analysis is to compute similarity of
expression over a set of libraries. Sequences showing similar expression
across the libraries are judged to be involved in the same network. The two PCC export
options compute these correlations and output files of extension ".pcc" (the raw correlation
scores) and ".sif" (requires a correlation threshold, SIF format as used by Cytoscape, though
an intermediate clustering algorithm is needed).  